Methods and apparatuses are provided for data transmission of a User Equipment (UE) in a communication system supporting HARQ. A Physical Downlink Control Channel (PDCCH) corresponding to a second cell is received in a first cell. An Uplink/Downlink (UL/DL) configuration of the first cell is identified as an Uplink (UL) reference UL/DL configuration, if the UE is configured with at least two cells including the first cell and the second cell, a PDCCH corresponding to the second cell is monitored on the first cell, and a pair of the UL/DL configuration of the first cell and a UL/DL configuration of the second cell is a predetermined set. A Physical Uplink Shared Channel (PUSCH) transmission is adjusted based on the identified UL reference UL/DL configuration.